The paper presents a significant advancement in quantum metrology by demonstrating universal quantum operations and ancilla-based readout for neutral atom optical clocks. The authors achieve high-fidelity two-qubit entangling gates with a fidelity of 99.62%, enabling the preparation of near-optimal entangled probe states and performing dual-quadrature readout. They also introduce ancilla-based quantum logic spectroscopy, allowing for repeated fast phase detection with minimal dead time. The system's ability to generate cascades of Greenberger-Horne-Zeilinger (GHZ) states and perform measurement-based Bell state preparation is highlighted. These advancements lay the foundation for hybrid processor-clock devices, combining quantum processors with quantum sensors, and point towards practical applications in precision measurements. The work addresses the challenge of achieving optimal sensitivity in the presence of noise, a key goal in quantum metrology, and demonstrates the potential for practical quantum-enhanced metrology.The paper presents a significant advancement in quantum metrology by demonstrating universal quantum operations and ancilla-based readout for neutral atom optical clocks. The authors achieve high-fidelity two-qubit entangling gates with a fidelity of 99.62%, enabling the preparation of near-optimal entangled probe states and performing dual-quadrature readout. They also introduce ancilla-based quantum logic spectroscopy, allowing for repeated fast phase detection with minimal dead time. The system's ability to generate cascades of Greenberger-Horne-Zeilinger (GHZ) states and perform measurement-based Bell state preparation is highlighted. These advancements lay the foundation for hybrid processor-clock devices, combining quantum processors with quantum sensors, and point towards practical applications in precision measurements. The work addresses the challenge of achieving optimal sensitivity in the presence of noise, a key goal in quantum metrology, and demonstrates the potential for practical quantum-enhanced metrology.